view screen_abricate_report.xml @ 1:45542cd244ad draft default tip

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"

<tool id="screen_abricate_report" name="Screen Abricate Report" version="0.1.0">
    <description>Screens an abricate report for genes of interest</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        '${__tool_directory__}/screen_abricate_report.py'
             '${abricate_report}'
             --screening_file '${screening_file.fields.path}'
             --screened_report '${screened_report}'
             --gene_detection_status '${gene_detection_status}'
    ]]></command>
    <inputs>
        <param name="abricate_report" type="data" format="tabular" />
        <param name="screening_file" type="select" format="tabular">
	    <options from_data_table="abricate_report_screening_files">
	        <validator type="no_options" message="No abricate report screening files are available" />
            </options>
	</param>
    </inputs>
    <outputs>
        <data name="screened_report" type="data" format="tabular" label="Screened Abricate Report" />
        <data name="gene_detection_status" type="data" format="tabular" label="Gene Detection Status" />
    </outputs>
    <tests>
        <test>
            <param name="screening_file" value="test_entry"/>
            <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/>
	    <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/>
	    <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
    <citations>
    </citations>
</tool>